discrepancy_core.hpp File Reference

#include <misc/discrepancy/discrepancy.hpp>
#include <objects/biblio/Auth_list.hpp>
#include <objects/biblio/Cit_sub.hpp>
#include <objects/general/Person_id.hpp>
#include <objects/macro/Suspect_rule_set.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/submit/Submit_block.hpp>
#include <objmgr/util/sequence.hpp>

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Classes
struct	CDiscrepancyCaseProps
class	CDiscrepancyCasePropsRef< _Name >
struct	CSimpleTypeObject< T >
class	CDiscrepancyItem
struct	CReportObjPtr
class	CReportNode
class	CDiscrepancyCore
class	CDiscrepancyPrivateData< _Name >
class	CDiscrepancyVisitorImpl< _Name >
struct	CSeqSummary
class	CDiscrepancyProductImpl
class	CDiscrepancyContext
struct	CDiscrepancyContext::CSeqdesc_vec
struct	CDiscrepancyContext::CSeqdesc_vec::iterator
struct	CDiscrepancyContext::CSeq_feat_vec
struct	CDiscrepancyContext::CSeq_feat_vec::iterator
struct	CDiscrepancyContext::CSeqdesc_run
struct	CDiscrepancyContext::CSeqdesc_run::iterator
struct	CDiscrepancyContext::CSeq_feat_run
struct	CDiscrepancyContext::CSeq_feat_run::iterator
struct	CDiscrepancyContext::CRefNode
struct	CDiscrepancyContext::CParseNode
class	CDiscrepancyObject
class	CReportObjFactory

Macros
#define	ADD_DISCREPANCY_TYPE(type)   vector<CDiscrepancyCore*> m_All_##type;
#define	DISCREPANCY_CASE_FULL(name, sname, type, group, descr, aliases_ptr)
#define	DISCREPANCY_CASE(name, type, group, descr)    DISCREPANCY_CASE_FULL(name, #name, type, group, descr, nullptr)
#define	DISCREPANCY_CASE0(name, sname, type, group, descr)    DISCREPANCY_CASE_FULL(name, sname, type, group, descr, nullptr)
#define	DISCREPANCY_CASE1(name, type, group, descr, ...)
#define	DISCREPANCY_SUMMARIZE(name)    template<> void CDiscrepancyVisitorImpl<eTestNames::name>::Summarize()
#define	DISCREPANCY_AUTOFIX(name)

Typedefs
typedef set< CReportObjPtr >	TReportObjectSet
typedef map< eTestNames, CRef< CDiscrepancyCore > >	TDiscrepancyCoreMap
typedef list< pair< CRef< CDiscrepancyObject >, string > >	TGenesList
	CDiscrepancyContext - manage and run the list of tests. More...
typedef map< string, TGenesList >	TGeneLocusMap

Functions
	USING_SCOPE (objects)
void	UnitTest_FLATFILE_FIND ()
	Checking that FLATFILE_FIND.inc is in sync with kSpellFixes If the array is changed, need to regenerate FLATFILE_FIND.inc: multipattern.exe -i FLATFILE_FIND.txt > FLATFILE_FIND.inc. More...

Macro Definition Documentation

ADD_DISCREPANCY_TYPE

#define ADD_DISCREPANCY_TYPE

(

type

)

vector<CDiscrepancyCore*> m_All_##type;

Definition at line 611 of file discrepancy_core.hpp.

DISCREPANCY_AUTOFIX

#define DISCREPANCY_AUTOFIX

(

name

)

Value:

    template<>                                                                                                      \
    CRef<CAutofixReport>                                                                                            \
    CDiscrepancyVisitorImpl<eTestNames::name>::Autofix(CDiscrepancyObject* obj, CDiscrepancyContext& context) const

Definition at line 952 of file discrepancy_core.hpp.

DISCREPANCY_CASE

#define DISCREPANCY_CASE	(		name,
			type,
			group,
			descr
	)		DISCREPANCY_CASE_FULL(name, #name, type, group, descr, nullptr)

Definition at line 937 of file discrepancy_core.hpp.

DISCREPANCY_CASE0

#define DISCREPANCY_CASE0	(		name,
			sname,
			type,
			group,
			descr
	)		DISCREPANCY_CASE_FULL(name, sname, type, group, descr, nullptr)

Definition at line 940 of file discrepancy_core.hpp.

DISCREPANCY_CASE1

#define DISCREPANCY_CASE1	(		name,
			type,
			group,
			descr,
			...
	)

Value:

    static constexpr std::initializer_list<const char*> g_aliases_ ##name = { __VA_ARGS__ };                        \
    DISCREPANCY_CASE_FULL(name, #name, type, group, descr, &g_aliases_ ##name)

Definition at line 943 of file discrepancy_core.hpp.

DISCREPANCY_CASE_FULL

#define DISCREPANCY_CASE_FULL	(		name,
			sname,
			type,
			group,
			descr,
			aliases_ptr
	)

Value:

    static constexpr CDiscrepancyCaseProps s_testcase_props_##name = {                                              \
        CDiscrepancyVisitorImpl<eTestNames::name>::Create,                                                          \
        eTestTypes::type, eTestNames::name, sname, descr, group, aliases_ptr};                                      \
    template<>                                                                                                      \
    const CDiscrepancyCaseProps*                                                                                    \
    CDiscrepancyCasePropsRef<eTestNames::name>::props = &s_testcase_props_##name;                                   \
    template<> void CDiscrepancyVisitorImpl<eTestNames::name>::Visit(NCBI_UNUSED CDiscrepancyContext& context)

Definition at line 928 of file discrepancy_core.hpp.

DISCREPANCY_SUMMARIZE

#define DISCREPANCY_SUMMARIZE

(

name

)

template<> void CDiscrepancyVisitorImpl<eTestNames::name>::Summarize()

Definition at line 948 of file discrepancy_core.hpp.

Typedef Documentation

TDiscrepancyCoreMap

typedef map<eTestNames, CRef<CDiscrepancyCore> > TDiscrepancyCoreMap

Definition at line 230 of file discrepancy_core.hpp.

TGeneLocusMap

typedef map<string, TGenesList> TGeneLocusMap

Definition at line 301 of file discrepancy_core.hpp.

TGenesList

typedef list<pair<CRef<CDiscrepancyObject>, string> > TGenesList

CDiscrepancyContext - manage and run the list of tests.

Definition at line 300 of file discrepancy_core.hpp.

TReportObjectSet

typedef set<CReportObjPtr> TReportObjectSet

Definition at line 149 of file discrepancy_core.hpp.

Function Documentation

UnitTest_FLATFILE_FIND()

void UnitTest_FLATFILE_FIND

(

)

Checking that FLATFILE_FIND.inc is in sync with kSpellFixes If the array is changed, need to regenerate FLATFILE_FIND.inc: multipattern.exe -i FLATFILE_FIND.txt > FLATFILE_FIND.inc.

Definition at line 1704 of file sequence_tests.cpp.

References eUnknown, FindFlatfileText(), i, kSpellFixes, kSpellFixesSize, SpellFixData::m_misspell, and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE().

USING_SCOPE()

USING_SCOPE

(

objects

)